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- PDB-5cnh: X-ray structure of perdeuterated wild-type TTR at 1.42A resolution -

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Basic information

Entry
Database: PDB / ID: 5cnh
TitleX-ray structure of perdeuterated wild-type TTR at 1.42A resolution
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / ATTR / prealbumin
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family ...Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsYee, A.W. / Moulin, M. / Mossou, E. / Haertlein, M. / Mitchell, E.P. / Cooper, J.B. / Forsyth, V.T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses.
Authors: Yee, A.W. / Moulin, M. / Breteau, N. / Haertlein, M. / Mitchell, E.P. / Cooper, J.B. / Boeri Erba, E. / Forsyth, V.T.
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)28,0732
Polymers28,0732
Non-polymers00
Water2,630146
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)56,1474
Polymers56,1474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6230 Å2
ΔGint-44 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.640, 85.793, 64.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

21B-223-

HOH

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Components

#1: Protein Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 14036.688 Da / Num. of mol.: 2 / Fragment: UNP residues 21-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.4M di-sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 21, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.419→64.158 Å / Num. all: 45102 / Num. obs: 45102 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.049 / Rsym value: 0.043 / Net I/av σ(I): 7.581 / Net I/σ(I): 15.6 / Num. measured all: 193286
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.42-1.54.31.3920.52761264270.7321.392198.6
1.5-1.594.20.8370.92581961450.4470.8371.799.7
1.59-1.74.30.4741.62517658170.2530.474399.7
1.7-1.834.30.2682.92344954180.1440.2685.299.8
1.83-2.014.20.1156.72108949770.0620.1151199.5
2.01-2.244.40.06212.32014145530.0330.06219.299.9
2.24-2.594.20.0418.71704340130.0210.0426.799.6
2.59-3.174.40.02625.71520034480.0140.02639.9100
3.17-4.494.20.01926.51143927220.010.01957.799.6
4.49-38.18440.02313631815820.0140.02361.199.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.8.0049refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PVL

4pvl


Resolution: 1.42→64.158 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.212 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 2268 5 %RANDOM
Rwork0.1518 ---
obs0.154 42792 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.88 Å2 / Biso mean: 29.133 Å2 / Biso min: 13.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å2-0 Å2
2--0.41 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.42→64.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 0 147 1939
Biso mean---41.09 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191872
X-RAY DIFFRACTIONr_bond_other_d0.0010.021718
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9462563
X-RAY DIFFRACTIONr_angle_other_deg0.9233976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74823.84678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.857158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212125
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02415
X-RAY DIFFRACTIONr_mcbond_it4.1512.35946
X-RAY DIFFRACTIONr_mcbond_other4.1233.423945
X-RAY DIFFRACTIONr_mcangle_it4.1743.5091186
X-RAY DIFFRACTIONr_rigid_bond_restr9.4631872
X-RAY DIFFRACTIONr_sphericity_bonded20.76951820
LS refinement shellResolution: 1.419→1.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 170 -
Rwork0.388 3050 -
all-3220 -
obs--97.08 %

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